From: Tamas Hegedus (
Date: Tue Oct 01 2019 - 12:10:48 CDT


It is not clear what is your real problem.

1. Network path analysis does not need netwrokSetup; you need subopt

2. However, for subopt you need the contact.dat as the input and you
generate it using a tcl script (see below) and config file (as in the
tutorial) (and you also need carma). You run this tcl script with vmd as
(use different directory for each of your trajectory):

vmd -dispdev text -eofexit < ./net_input.tcl > net_output.log &&


set DIR /opt/vmd-1.9.3/lib/plugins/noarch/tcl/networkview1.41
set sfile_list "adjacencyMatrix.tcl  communityNetwork.tcl
networkSetup.tcl  networkViewGui.tcl  networkView.tcl  pkgIndex.tcl

foreach sfile $sfile_list {
     source "$DIR/$sfile"

networkSetup ./network.config

If you need further help, let me know

Bests, Tamas

On 10/1/19 11:52 AM, Naveen BK wrote:
> Dear all,
> I was conducting network path analysis. I have multiple trajectories
> and I want to do it for all. But I want to run it in command mode with
> scripts but not the way explained in the tutorial. Once I get all the
> output files using scripts then it will be easy to load and visualise.
> But when I tried with command line networkSetup flag was not
> recognised. Please help me out to sort this.
> Thanks and Regards,
> Naveen BK,
> MSc in bioinformatics,
> +918123474717.